Model gets squished because of Spline IK
This is just a workaround as this behaviour seems more like a bug and this solution can break the position of the controllers depending on your setup, but you can set the Spline IK constrain on a copy of the bone chain and use it as an intermediary mechanical rig. I'm not at home right now so I'll upload later. But the setup is simple:


Make a copy of the chain that receives the Spline IK.
Set it up so it receives the Spline IK instead.
Reparent or reconstrain the Control Rig to the new chain.
Remove the Spline IK constrain from the original one.
Add copy rotation constraints (and an optional copy location constrain to the root of the chain)  from the new bone chain to the original one.


Now your chain receives the rotations from your controllers but preserve their scales.